mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 33,417 | C→T | 3.2% | R867R (CGC→CGT) | carB → | carbamoyl‑phosphate synthase large subunit |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 358,474 | Δ1 bp | 3.2% | coding (217/900 nt) | cynR ← | transcriptional activator of cyn operon, autorepressor |
| RA | 375,275 | C→T | 4.1% | intergenic (+394/‑184) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| JC | 417,075 | (TCATAAATCTG)2→1 | 27.6% | intergenic (‑123/‑57) | sbcD ← / → phoB | exonuclease, dsDNA, ATP‑dependent/response regulator in two‑component regulatory system with PhoR |
| JC | 417,256 | Δ17 bp | 4.6% | coding (115‑131/690 nt) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 417,753 | Δ1 bp | 100% | coding (612/690 nt) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 431,563 | Δ1 bp | 3.0% | coding (451/885 nt) | tsx ← | nucleoside channel, receptor of phage T6 and colicin K |
| RA | 465,806 | T→A | 3.7% | I503L (ATA→TTA) | ybaE ← | putative ABC transporter periplasmic binding protein |
| RA | 495,015 | A→G | 3.3% | intergenic (+5/‑105) | recR → / → htpG | gap repair protein/protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent, heat‑shock protein, ATPase |
| RA | 526,713 | G→A | 3.2% | A1151A (GCG→GCA) | rhsD → | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| RA | 619,699 | G→A | 3.9% | L167L (CTC→CTT) | fepC ← | ferrienterobactin ABC transporter ATPase |
| RA | 702,000 | T→G | 5.4% | H251P (CAT→CCT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,306 | C→T | 27.3% | R149H (CGT→CAT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,331 | Δ1 bp | 34.6% | coding (421/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,390 | T→G | 17.9% | H121P (CAT→CCT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| JC | 1,159,286:1 | +GTA | 100% | coding (1418/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,246,804 | G→A | 3.7% | Y191Y (TAC→TAT) | treA ← | periplasmic trehalase |
| JC | 1,374,040:1 | +TTC | 3.2% | coding (819/882 nt) | ycjO → | putative sugar ABC transporter permease |
| RA | 1,395,089 | G→T | 2.9% | F278L (TTC→TTA) | ynaI ← | mechanosensitive channel protein, very small conductance |
| RA | 1,466,201 | T→C | 6.4% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,592,233 | T→A | 3.1% | L70L (CTA→CTT) | hipB ← | antitoxin of HipAB toxin‑antitoxin system |
| RA | 1,701,569 | A→T | 4.0% | M205L (ATG→TTG) | malY → | PLP‑dependent beta‑cystathionase and maltose regulon regulator |
| RA | 1,726,004 | G→A | 100% | intergenic (‑84/‑19) | ydhL ← / → nemR | DUF1289 family protein/transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,756,980 | Δ1 bp | 11.9% | coding (1283/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,789,902 | T→C | 3.7% | E448G (GAG→GGG) | ydiU ← | UPF0061 family protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,352,559 | G→T | 11.2% | intergenic (‑187/‑86) | glpT ← / → glpA | sn‑glycerol‑3‑phosphate transporter/anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| RA | 2,555,586 | T→C | 3.0% | E47E (GAA→GAG) | eutK ← | putative ethanol utilization carboxysome structural protein |
| RA | 2,638,239 | C→A | 4.1% | D138Y (GAT→TAT) | bamB ← | BamABCDE complex OM biogenesis lipoprotein |
| RA | 2,671,880 | C→T | 3.3% | L220L (CTG→TTG) | hcaB → | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase |
| RA | 2,776,227 | A→T | 2.8% | E104V (GAA→GTA) | yfjX → | CP4‑57 prophage, putative antirestriction protein |
| RA | 2,957,249 | T→C | 2.9% | E545G (GAG→GGG) | ptrA ← | protease III |
| RA | 2,976,907 | A→C | 100% | E104A (GAG→GCG) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 3,092,108 | C→T | 3.7% | A78V (GCC→GTC) | gshB → | glutathione synthetase |
| RA | 3,093,034 | G→C | 2.8% | A34P (GCA→CCA) | yqgE → | uncharacterized protein |
| RA | 3,099,915 | Δ1 bp | 2.6% | coding (812/1047 nt) | ansB ← | periplasmic L‑asparaginase 2 |
| RA | 3,255,864 | G→A | 3.2% | G262G (GGC→GGT) | yhaM ← | putative L‑serine dehydratase alpha chain |
| RA | 3,455,872 | A→G | 6.7% | T99T (ACA→ACG) | gspC → | general secretory pathway component, cryptic |
| RA | 3,508,554 | T→C | 3.3% | H12R (CAT→CGT) | php ← | phosphotriesterase homology protein |
| RA | 3,512,273 | T→C | 5.7% | K24E (AAG→GAG) | yhfZ ← | putative DNA‑binding transcriptional regulator |
| RA | 3,591,800 | A→G | 3.7% | Y175Y (TAT→TAC) | ugpB ← | sn‑glycerol‑3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,661,410 | T→A | 2.7% | I333N (ATC→AAC) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,678,821 | G→A | 2.6% | R122R (CGC→CGT) | yhjH ← | cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,521 | C→G | 21.6% | L29V (CTG→GTG) | yidX → | putative lipoprotein |
| RA | 3,875,524 | G→T | 15.6% | V30F (GTT→TTT) | yidX → | putative lipoprotein |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| RA | 3,941,034 | T→C | 3.0% | E98G (GAG→GGG) | yieP ← | putative transcriptional regulator |
| RA | 3,966,735 | G→A | 10.8% | G107D (GGT→GAT) | rho → | transcription termination factor |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,171,647 | A→C | 100% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,178,222 | T→C | 8.6% | S161P (TCT→CCT) | nusG → | transcription termination factor |
| RA | 4,181,850 | A→C | 12.0% | K203Q (AAA→CAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,285,336 | A→T | 2.6% | intergenic (‑124/+76) | yjcH ← / ← acs | DUF485 family inner membrane protein/acetyl‑CoA synthetase |
| RA | 4,295,833 | T→C | 12.0% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 9.9% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 40.8% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 46.3% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,571,396 | C→T | 2.9% | P60P (CCG→CCA) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978461 | 1979382 | 922 | 46 [42] | [43] 47 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 3797895 | 3799779 | 1885 | 46 [44] | [44] 46 | [waaL]–[waaZ] | [waaL], waaU, [waaZ] |
| * | * | ÷ | NC_000913 | 3804144 | 3805247 | 1104 | 50 [45] | [44] 49 | waaS–[waaP] | waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4110664 | 4111574 | 911 | 48 [44] | [45] 46 | [cdh]–tpiA | [cdh], tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 93 (0.840) | 67/522 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 258674 | NA (NA) | 10 (0.090) | 10/520 | NT | 8.4% | intergenic (+775/‑2) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | 465151 = | 109 (0.990) | coding (397/696 nt) | queC | 7‑cyano‑7‑deazaguanine (preQ0) synthase, queuosine biosynthesis | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 4 (0.040) | 4/496 | NT | NA | coding (111/300 nt) | insE1 | IS3 transposase A |
| ? | NC_000913 | 315627 = | NA (NA) | coding (41/867 nt) | insF1 | IS3 transposase B | |||||
| * | ? | NC_000913 | = 805887 | 109 (0.990) | 3 (0.030) | 3/508 | NT | 2.8% | noncoding (84/178 nt) | REP72 (repetitive extragenic palindromic) element, contains 4 REP sequences | REP72 (repetitive extragenic palindromic) element, contains 4 REP sequences |
| ? | NC_000913 | = 805898 | 105 (0.980) | noncoding (95/178 nt) | REP72 (repetitive extragenic palindromic) element, contains 4 REP sequences | REP72 (repetitive extragenic palindromic) element, contains 4 REP sequences | |||||
| * | ? | NC_000913 | 1207790 = | 41 (0.370) | 44 (0.420) | 37/490 | NT | 49.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 52 (0.500) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 39 (0.350) | 80 (0.770) | 55/490 | NT | 64.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 52 (0.500) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 99 (0.890) | 70/522 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1299175 = | 84 (0.760) | 4 (0.040) | 4/522 | NT | 4.5% | coding (578/648 nt) | ychE | UPF0056 family inner membrane protein |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 67 (0.610) | 55/514 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1395088 | 108 (0.980) | 3 (0.030) | 3/508 | NT | 2.8% | coding (835/1032 nt) | ynaI | mechanosensitive channel protein, very small conductance |
| ? | NC_000913 | = 1395094 | 106 (0.980) | coding (829/1032 nt) | ynaI | mechanosensitive channel protein, very small conductance | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 26 (0.240) | 18/506 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 36 (0.330) | 24/522 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 82 (0.740) | 53/522 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2374947 = | 83 (0.750) | 20 (0.180) | 19/522 | NT | 19.4% | coding (55/1356 nt) | menE | O‑succinylbenzoate‑CoA ligase |
| ? | NC_000913 | = 2515612 | NA (NA) | intergenic (+171/+29) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase | |||||
| * | ? | NC_000913 | = 2374957 | 87 (0.790) | 10 (0.090) | 8/514 | NT | 10.5% | coding (45/1356 nt) | menE | O‑succinylbenzoate‑CoA ligase |
| ? | NC_000913 | 2514275 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||
| * | ? | NC_000913 | 2375822 = | 76 (0.690) | 85 (0.780) | 59/514 | NT | 53.2% | coding (139/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | = 2515611 | NA (NA) | intergenic (+170/+30) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase | |||||
| * | ? | NC_000913 | = 2375833 | 74 (0.670) | 69 (0.630) | 51/514 | NT | 48.6% | coding (128/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | 2514275 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||
| * | ? | NC_000913 | 3467129 = | 50 (0.450) | 4 (0.040) | 4/506 | NT | 7.7% | intergenic (‑140/+29) | bfd/chiA | bacterioferritin‑associated ferredoxin/periplasmic endochitinase |
| ? | NC_000913 | 3467151 = | 48 (0.450) | intergenic (‑162/+7) | bfd/chiA | bacterioferritin‑associated ferredoxin/periplasmic endochitinase | |||||
| * | ? | NC_000913 | 3652035 = | NA (NA) | 13 (0.120) | 13/522 | NT | 22.8% | intergenic (+5/+146) | yhiS/insH1 | pseudogene/IS5 transposase and trans‑activator |
| ? | NC_000913 | = 3922631 | 44 (0.400) | intergenic (‑192/+425) | atpI/rsmG | ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent, glucose‑inhibited cell‑division protein | |||||
| * | ? | NC_000913 | = 3653229 | NA (NA) | 21 (0.190) | 20/522 | NT | 32.8% | intergenic (‑32/‑1) | insH1/yhiS | IS5 transposase and trans‑activator/pseudogene |
| ? | NC_000913 | 3922628 = | 43 (0.390) | intergenic (‑189/+428) | atpI/rsmG | ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent, glucose‑inhibited cell‑division protein | |||||
| * | ? | NC_000913 | 4285325 = | NA (NA) | 4 (0.040) | 4/510 | NT | 2.8% | noncoding (25/77 nt) | REP320 (repetitive extragenic palindromic) element, contains 2 REP sequences | REP320 (repetitive extragenic palindromic) element, contains 2 REP sequences |
| ? | NC_000913 | 4285352 = | 140 (1.300) | noncoding (52/77 nt) | REP320 (repetitive extragenic palindromic) element, contains 2 REP sequences | REP320 (repetitive extragenic palindromic) element, contains 2 REP sequences | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 20 (0.210) | 6/444 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||